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PloS One 2017Avian influenza or bird flu is a highly contagious acute viral disease that can occur in epidemics and cross-border forms in poultry and wild birds. The characteristics... (Review)
Review
Avian influenza or bird flu is a highly contagious acute viral disease that can occur in epidemics and cross-border forms in poultry and wild birds. The characteristics of avian influenza viruses (AIVs) allow the emergence of new viral variants, some with zoonotic and pandemic potential. AIVs have been identified in Latin America; however, there is a lack of understanding of these viruses at the regional level. We performed a systematic literature review on serological or molecular evidence of AIVs circulation in Latin America. Methods were designed based on the PRISMA and STROME guidelines. Only peer-reviewed studies published between 2000 to 2015 and data was analysed based on country, viral subtype, avian species, and phylogenetic origins. From 271 studies initially found only twenty-six met our inclusion criteria. Evidence of AIVs infection was found in most Latin American countries, with Mexico as the country with the largest number of conducted studies and reported cases during the period analysed, followed by Chile and Argentina. Most of the AIVs were early reported through surveillance systems and at least 14 different subtypes of influenza viruses were reported in birds, and the presence of both low (92.9%) and high (7.1%) pathogenic AIVs was shown in Latin America. Of the reported AIVs in Latin America, 43.7% belong to migratory birds, 28.1% to local wild birds, and 28.1% to poultry. The migratory bird population mainly comprises families belonging to the orders Anseriformes and Charadriformes. We highlight the importance of epidemiological surveillance systems and the possible role of different migratory birds in the transmission of AIVs within the Americas. Our findings demonstrate the limited information on AIVs in Latin America and highlight the need of more studies on AIVs at the regional level, particularly those focused on identifying the endemic subtypes in regional wild birds.
Topics: Animal Migration; Animals; Animals, Wild; Genotype; Influenza A virus; Influenza in Birds; Latin America; Poultry
PubMed: 28632771
DOI: 10.1371/journal.pone.0179573 -
PloS One 2017The emergence of the 2009 influenza pandemic virus with a swine origin stressed the importance of improving influenza surveillance in swine populations. The objectives... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
The emergence of the 2009 influenza pandemic virus with a swine origin stressed the importance of improving influenza surveillance in swine populations. The objectives of this systematic review and meta-analysis were to describe epidemiological features of swine influenza (SI) across the world and identify factors impacting swine influenza virus surveillance.
METHODS
The systematic review followed the PRISMA guidelines. Articles published after 1990 containing data on SI on pig and herd-level seroprevalence, isolation and detection rates, and risk factors were included. Meta-regression analyses using seroprevalence and virological rates were performed.
RESULTS
A total of 217 articles were included. Low avian influenza (AI) seroprevalence (means pig = 4.1%; herd = 15%) was found, showing that AIV do not readily establish themselves in swine while SIV seroprevalence was usually high across continents (influenza A means pig = 32.6-87.8%; herd = 29.3-100%). Higher pig density and number of pigs per farm were shown by the meta-regression analyses and/or the risk factor articles to be associated with higher SI seroprevalence. Lower seroprevalence levels were observed for countries with low-to-medium GDP. These results suggest that larger industrial farms could be more at risk of SIV circulation. Sampling swine with influenza-like illness (ILI) was positively associated with higher isolation rates; most studies in Europe, Latin and North America were targeting swine with ILI.
CONCLUSIONS
To improve understanding of SI epidemiology, standardization of the design and reporting of SI epidemiological studies is desirable. Performance of SI surveillance systems in low-to-medium GDP countries should be evaluated to rule out technical issues linked to lower observed SIV prevalence. Targeting certain swine age groups, farming systems and swine with ILI may improve the surveillance cost-effectiveness. However, focusing on pigs with ILI may bias virus detection against strains less virulent for swine but which may be important as pandemic threats.
Topics: Animals; Europe; Humans; Influenza A Virus, H1N1 Subtype; Influenza, Human; North America; Orthomyxoviridae Infections; Seroepidemiologic Studies; Swine; Swine Diseases; Zoonoses
PubMed: 28591202
DOI: 10.1371/journal.pone.0179044 -
PloS One 2016Avian influenza viruses are able to persist in the environment, in-between the transmission of the virus among its natural hosts. Quantifying the environmental factors... (Meta-Analysis)
Meta-Analysis Review
Avian influenza viruses are able to persist in the environment, in-between the transmission of the virus among its natural hosts. Quantifying the environmental factors that affect the persistence of avian influenza virus is important for influencing our ability to predict future outbreaks and target surveillance and control methods. We conducted a systematic review and quantitative meta-analysis of the environmental factors that affect the decay of low pathogenic avian influenza virus (LPAIV) in water. Abiotic factors affecting the persistence of LPAIV have been investigated for nearly 40 years, yet published data was produced by only 26 quantitative studies. These studies have been conducted by a small number of principal authors (n = 17) and have investigated a narrow range of environmental conditions, all of which were based in laboratories with limited reflection of natural conditions. The use of quantitative meta-analytic techniques provided the opportunity to assess persistence across a greater range of conditions than each individual study can achieve, through the estimation of mean effect-sizes and relationships among multiple variables. Temperature was the most influential variable, for both the strength and magnitude of the effect-size. Moderator variables explained a large proportion of the heterogeneity among effect-sizes. Salinity and pH were important factors, although future work is required to broaden the range of abiotic factors examined, as well as including further diurnal variation and greater environmental realism generally. We were unable to extract a quantitative effect-size estimate for approximately half (50.4%) of the reported experimental outcomes and we strongly recommend a minimum set of quantitative reporting to be included in all studies, which will allow robust assimilation and analysis of future findings. In addition we suggest possible means of increasing the applicability of future studies to the natural environment, and evaluating the biological content of natural waterbodies.
Topics: Animals; Birds; Disease Outbreaks; Influenza A virus; Influenza in Birds; Salinity; Temperature; Water Microbiology
PubMed: 27736884
DOI: 10.1371/journal.pone.0161929 -
One Health (Amsterdam, Netherlands) Dec 2016Live poultry markets (LPMs) pose a threat to public health by promoting the amplification and dissemination of avian influenza viruses (AIVs) and by providing the ideal...
BACKGROUND
Live poultry markets (LPMs) pose a threat to public health by promoting the amplification and dissemination of avian influenza viruses (AIVs) and by providing the ideal setting for zoonotic influenza transmission.
OBJECTIVE
This review assessed the impact of different interventions implemented in LPMs to control the emergence of zoonotic influenza.
METHODS
Publications were identified through a systematic literature search in the PubMed, MEDLINE and Web of Science databases. Eligible studies assessed the impact of different interventions, such as temporary market closure or a ban on holding poultry overnight, in reducing i) AIV-detection rates in birds and the market environment or ii) influenza incidence in humans. Unpublished literature, reviews, editorials, cross-sectional studies, theoretical models and publications in languages other than English were excluded. Relevant findings were extracted and critically evaluated. For the comparative analysis of findings across studies, standardized outcome measures were computed as i) the relative risk reduction (RRR) of AIV-detection in LPMs and ii) incidence rate ratios (IRRs) of H7N9-incidence in humans.
RESULTS
A total of 16 publications were identified and reviewed. Collectively, the data suggest that AIV-circulation can be significantly reduced in the LPM-environment and among market-birds through (i) temporary LPM closure, (ii) periodic rest days (iii) market depopulation overnight and (iv) improved hygiene and disinfection. Overall, the findings indicate that the length of stay of poultry in the market is a critical control point to interrupt the AIV-replication cycle within LPMs. In addition, temporary LPM closure was associated with a significant reduction of the incidence of zoonotic influenza. The interpretation of these findings is limited by variations in the implementation of interventions. In addition, some of the included studies were of ecologic nature or lacked an inferential framework, which might have lead to cosiderable confounding and bias.
CONCLUSIONS
The evidence collected in this review endorses permanent LPM-closure as a long-term objective to reduce the zoonotic risk of avian influenza, although its economic and socio-political implications favour less drastic interventions, e.g. weekly rest days, for implementation in the short-term.
PubMed: 27213177
DOI: 10.1016/j.onehlt.2016.03.002 -
The Lancet. Infectious Diseases Jul 2016Avian influenza A H5N1 viruses have caused many, typically severe, human infections since the first human case was reported in 1997. However, no comprehensive... (Review)
Review
Avian influenza A H5N1 viruses have caused many, typically severe, human infections since the first human case was reported in 1997. However, no comprehensive epidemiological analysis of global human cases of H5N1 from 1997 to 2015 exists. Moreover, few studies have examined in detail the changing epidemiology of human H5N1 cases in Egypt, especially given the outbreaks since November, 2014, which have the highest number of cases ever reported worldwide in a similar period. Data on individual patients were collated from different sources using a systematic approach to describe the global epidemiology of 907 human H5N1 cases between May, 1997, and April, 2015. The number of affected countries rose between 2003 and 2008, with expansion from east and southeast Asia, then to west Asia and Africa. Most cases (67·2%) occurred from December to March, and the overall case-fatality risk was 483 (53·5%) of 903 cases which varied across geographical regions. Although the incidence in Egypt has increased dramatically since November, 2014, compared with the cases beforehand, there were no significant differences in the fatality risk, history of exposure to poultry, history of patient contact, and time from onset to hospital admission in the recent cases.
Topics: Animals; Disease Outbreaks; Global Health; Humans; Incidence; Influenza A Virus, H5N1 Subtype; Influenza in Birds; Influenza, Human; Poultry
PubMed: 27211899
DOI: 10.1016/S1473-3099(16)00153-5 -
PloS One 2016Understanding the evolutionary dynamics of influenza viruses is essential to control both avian and human influenza. Here, we analyze host-specific and segment-specific... (Review)
Review
Understanding the evolutionary dynamics of influenza viruses is essential to control both avian and human influenza. Here, we analyze host-specific and segment-specific Tajima's D trends of influenza A virus through a systematic review using viral sequences registered in the National Center for Biotechnology Information. To avoid bias from viral population subdivision, viral sequences were stratified according to their sampling locations and sampling years. As a result, we obtained a total of 580 datasets each of which consists of nucleotide sequences of influenza A viruses isolated from a single population of hosts at a single sampling site within a single year. By analyzing nucleotide sequences in the datasets, we found that Tajima's D values of viral sequences were different depending on hosts and gene segments. Tajima's D values of viruses isolated from chicken and human samples showed negative, suggesting purifying selection or a rapid population growth of the viruses. The negative Tajima's D values in rapidly growing viral population were also observed in computer simulations. Tajima's D values of PB2, PB1, PA, NP, and M genes of the viruses circulating in wild mallards were close to zero, suggesting that these genes have undergone neutral selection in constant-sized population. On the other hand, Tajima's D values of HA and NA genes of these viruses were positive, indicating HA and NA have undergone balancing selection in wild mallards. Taken together, these results indicated the existence of unknown factors that maintain viral subtypes in wild mallards.
Topics: Algorithms; Animals; Birds; Computational Biology; Computer Simulation; Disease Outbreaks; Evolution, Molecular; Genes, Viral; Host-Pathogen Interactions; Humans; Influenza A virus; Influenza in Birds; Influenza, Human; Models, Statistical; Mutation
PubMed: 26760775
DOI: 10.1371/journal.pone.0147021 -
BMC Infectious Diseases Jan 2016Most previous evolutionary studies of influenza A have focussed on genetic drift, or reassortment of specific gene segments, hosts or subtypes. We conducted a systematic... (Review)
Review
BACKGROUND
Most previous evolutionary studies of influenza A have focussed on genetic drift, or reassortment of specific gene segments, hosts or subtypes. We conducted a systematic literature review to identify reported claimed reassortant influenza A lineages with genomic data available in GenBank, to obtain 646 unique first-report isolates out of a possible 20,781 open-access genomes.
RESULTS
After adjusting for correlations, only: swine as host, China, Europe, Japan and years between 1997 and 2002; remained as significant risk factors for the reporting of reassortant viral lineages. For swine H1, more reassortants were observed in the North American H1 clade compared with the Eurasian avian-like H1N1 clade. Conversely, for avian H5 isolates, a higher number of reported reassortants were observed in the European H5N2/H3N2 clade compared with the H5N2 North American clade.
CONCLUSIONS
Despite unavoidable biases (publication, database choice and upload propensity) these results synthesize a large majority of the current literature on novel reported influenza A reassortants and are a potentially useful prerequisite to inform further algorithmic studies.
Topics: Animals; Genetic Drift; Humans; Influenza A Virus, H1N1 Subtype; Influenza A Virus, H3N2 Subtype; Influenza A Virus, H5N2 Subtype; Influenza, Human; Phylogeny; Reassortant Viruses
PubMed: 26732146
DOI: 10.1186/s12879-015-1298-9 -
Clinical Microbiology and Infection :... Oct 2015Administration of corticosteroids to patients affected by influenza virus, especially pandemic avian influenza virus, although relatively common, remains controversial.... (Meta-Analysis)
Meta-Analysis Review
Administration of corticosteroids to patients affected by influenza virus, especially pandemic avian influenza virus, although relatively common, remains controversial. A systematic review and meta-analysis was performed to assess the impact of corticosteroid treatment on outcomes of patients with influenza virus infection. The PubMed, EMBASE, Web of Science and Cochrane Library databases were searched up to February, 2015. Studies comparing corticosteroid treatment with no corticosteroid treatment in patients with influenza virus infection were included. The primary outcomes assessed were the association of mortality and nosocomial infection with corticosteroid treatment. Two authors independently extracted the data. ORs and weighted mean differences (WMDs) were used to describe dichotomous data and continuous data, respectively. Nineteen studies with 4916 patients were included in this meta-analysis. The results showed that corticosteroid treatment was significantly associated with mortality (OR 1.98, 95% CI 1.62-2.43, p < 0.00001) and nosocomial infection (OR 3.16, 95% CI 2.09-4.78, p < 0.00001). The durations of mechanical ventilation (WMD 3.82, 95% CI 1.49-6.15, p 0.001) and intensive-care unit stay (WMD 4.78, 95% CI 2.27-7.29, p 0.0002) were both markedly longer in the corticosteroid treatment group than in the control group. These findings suggest that routine steroid use may not be ideal for influenza virus infection. However, these results are derived from observational studies, with some important biases. They should be examined in future sufficiently powered randomized trials.
Topics: Adrenal Cortex Hormones; Anti-Inflammatory Agents; Cross Infection; Humans; Influenza, Human; Length of Stay; Respiration, Artificial; Survival Analysis; Treatment Outcome
PubMed: 26123860
DOI: 10.1016/j.cmi.2015.06.022 -
The Journal of Infectious Diseases Aug 2015Given that influenza A(H9N2) is recognized as a pandemic threat, we evaluated the overall burden of influenza A(H9N2) infections among avian-exposed human populations. (Meta-Analysis)
Meta-Analysis Review
INTRODUCTION
Given that influenza A(H9N2) is recognized as a pandemic threat, we evaluated the overall burden of influenza A(H9N2) infections among avian-exposed human populations.
METHODS
We performed a systematic search of PubMed, AGRICOLA, and CAB Abstracts databases for literature published during 1997-2013. Studies reporting serological evidence of human influenza A(H9N2) infection among avian-exposed populations were included. We used a World Health Organization (WHO)-recommended case definition for serological evidence of infection based on results of hemagglutination inhibition (HI) and microneutralization (MN) assays. We calculated overall seroprevalence through a random effects meta-analysis model.
RESULTS
Seroprevalence data reported by the studies ranged from 1% to 43% (median, 9%) by HI, which was not significantly different from the seroprevalence estimated through the WHO-recommended case definition (median, 1.3%; range, 0.5%-42.6%). Reported seroprevalence by MN ranged from 0.6% to 9% (median, 2.7%), which was greater than the seroprevalence estimated through the WHO-recommended case definition (median, 0.3%; range, 0.1%-1.4%).
CONCLUSIONS
A small proportion of avian-exposed humans had evidence of influenza A(H9N2) infection. As the virus has a near global distribution in poultry, it seems likely that present surveillance efforts are missing mild or asymptomatic infections among avian-exposed persons. It seems prudent to closely monitor avian-exposed populations for influenza A(H9N2) infection to provide prepandemic warnings.
Topics: Animals; Antibodies, Viral; Humans; Influenza A Virus, H9N2 Subtype; Influenza, Human; Seroepidemiologic Studies; Zoonoses
PubMed: 25712969
DOI: 10.1093/infdis/jiv109